.TH minimap2 1 "11 November 2017" "minimap2-2.5 (r572)" "Bioinformatics tools"
.SH NAME
.PP
minimap2 - mapping and alignment between collections of DNA sequences
.SH SYNOPSIS
* Indexing the target sequences (optional):
.RS 4
minimap2
.RB [ -x
.IR preset ]
.B -d
.I target.mmi
.I target.fa
.br
minimap2
.RB [ -H ]
.RB [ -k
.IR kmer ]
.RB [ -w
.IR miniWinSize ]
.RB [ -I
.IR batchSize ]
.B -d
.I target.mmi
.I target.fa
.RE

* Long-read alignment with CIGAR:
.RS 4
minimap2
.B -a
.RB [ -x
.IR preset ]
.I target.mmi
.I query.fa
>
.I output.sam
.br
minimap2
.B -c
.RB [ -H ]
.RB [ -k
.IR kmer ]
.RB [ -w
.IR miniWinSize ]
.RB [ ... ]
.I target.fa
.I query.fa
>
.I output.paf
.RE

* Long-read overlap without CIGAR:
.RS 4
minimap2
.B -x
ava-ont
.RB [ -t
.IR nThreads ]
.I target.fa
.I query.fa
>
.I output.paf
.RE
.SH DESCRIPTION
.PP
Minimap2 is a fast sequence mapping and alignment program that can find
overlaps between long noisy reads, or map long reads or their assemblies to a
reference genome optionally with detailed alignment (i.e. CIGAR). At present,
it works efficiently with query sequences from a few kilobases to ~100
megabases in length at a error rate ~15%. Minimap2 outputs in the PAF or the
SAM format.
.SH OPTIONS
.SS Indexing options
.TP 10
.BI -k \ INT
Minimizer k-mer length [15]
.TP
.BI -w \ INT
Minimizer window size [2/3 of k-mer length]. A minimizer is the smallest k-mer
in a window of w consecutive k-mers.
.TP
.B -H
Use homopolymer-compressed (HPC) minimizers. An HPC sequence is constructed by
contracting homopolymer runs to a single base. An HPC minimizer is a minimizer
on the HPC sequence.
.TP
.BI -I \ NUM
Load at most
.I NUM
target bases into RAM for indexing [4G]. If there are more than
.I NUM
bases in
.IR target.fa ,
minimap2 needs to read
.I query.fa
multiple times to map it against each batch of target sequences.
.I NUM
may be ending with k/K/m/M/g/G. NB: mapping quality is incorrect given a
multi-part index.
.TP
.BI -d \ FILE
Save the minimizer index of
.I target.fa
to
.I FILE
[no dump]. Minimap2 indexing is fast. It can index the human genome in a couple
of minutes. If even shorter startup time is desired, use this option to save
the index. Indexing options are fixed in the index file. When an index file is
provided as the target sequences, options
.BR -H ,
.BR -k ,
.BR -w ,
.B -I
will be effectively overridden by the options stored in the index file.
.SS Mapping options
.TP 10
.BI -f \ FLOAT
Ignore top
.I FLOAT
fraction of most frequent minimizers [0.0002]
.TP
.BI -g \ INT
Stop chain enlongation if there are no minimizers in
.IR INT -bp
[10000].
.TP
.BI -r \ INT
Bandwidth used in chaining and DP-based alignment [500]. This option
approximately controls the maximum gap size.
.TP
.BI -n \ INT
Discard chains consisting of
.RI < INT
number of minimizers [3]
.TP
.BI -m \ INT
Discard chains with chaining score
.RI < INT
[40]. Chaining score equals the approximate number of matching bases minus a
concave gap penalty. It is computed with dynamic programming.
.TP
.B -X
Perform all-vs-all mapping. In this mode, if the query sequence name is
lexicographically larger than the target sequence name, the hits between them
will be suppressed; if the query sequence name is the same as the target name,
diagonal minimizer hits will also be suppressed.
.TP
.BI -p \ FLOAT
Minimal secondary-to-primary score ratio to output secondary mappings [0.8].
Between two chains overlaping over half of the shorter chain (controlled by
.BR --mask-level ),
the chain with a lower score is secondary to the chain with a higher score.
If the ratio of the scores is below
.IR FLOAT ,
the secondary chain will not be outputted or extended with DP alignment later.
.TP
.BI -N \ INT
Output at most
.I INT
secondary alignments [5]. This option has no effect when
.B -X
is applied.
.TP
.BI -G \ NUM
Maximum gap on the reference (effective with
.BR -xsplice / --splice ).
This option also changes the chaining and alignment band width to
.IR NUM .
Increasing this option slows down spliced alignment. [200k]
.TP
.BI -F \ NUM
Maximum fragment length (aka insert size; effective with
.BR -xsr / --frag)
[800]
.TP
.BI --max-chain-skip \ INT
A heuristics that stops chaining early [50]. Minimap2 uses dynamic programming
for chaining. The time complexity is quadratic in the number of seeds. This
option makes minimap2 exits the inner loop if it repeatedly sees seeds already
on chains. Set
.I INT
to a large number to switch off this heurstics.
.TP
.B --no-long-join
Disable the long gap patching heuristic. When this option is applied, the
maximum alignment gap is mostly controlled by
.BR -r .
.TP
.B --splice
Enable the splice alignment mode.
.TP
.B --sr
Enable short-read alignment heuristics. In the short-read mode, minimap2
applies a second round of chaining with a higher minimizer occurrence threshold
if no good chain is found. In addition, minimap2 attempts to patch gaps between
seeds with ungapped alignment.
.TP
.BR --frag [= no | yes ]
Whether to enable the fragment mode [no]
.SS Alignment options
.TP 10
.BI -A \ INT
Matching score [2]
.TP
.BI -B \ INT
Mismatching penalty [4]
.TP
.BI -O \ INT1[,INT2]
Gap open penalty [4,24]. If
.I INT2
is not specified, it is set to
.IR INT1 .
.TP
.BI -E \ INT1[,INT2]
Gap extension penalty [2,1]. A gap of length
.I k
costs
.RI min{ O1 + k * E1 , O2 + k * E2 }.
In the splice mode, the second gap penalties are not used.
.TP
.BI -C \ INT
Cost for a non-canonical GT-AG splicing (effective with
.BR --splice )
[0]
.TP
.BI -z \ INT
Break an alignment if the running score drops too quickly along the diagonal of
the DP matrix (diagonal X-drop, or Z-drop) [400]. Increasing the value improves
the contiguity of the alignment at the cost of poor alignment in the middle
(e.g. caused by a long inversion).
.TP
.BI -s \ INT
Minimal peak DP alignment score to output [40]. The peak score is computed from
the final CIGAR. It is the score of the max scoring segment in the alignment
and may be different from the total alignment score.
.TP
.BI -u \ CHAR
How to find canonical splicing sites GT-AG -
.BR f :
transcript strand;
.BR b :
both strands;
.BR n :
no attempt to match GT-AG [n]
.TP
.BI --end-bonus \ INT
Score bonus when alignment extends to the end of the query sequence [0].
.TP
.BR --splice-flank [= yes | no ]
Assume the next base to a
.B GT
donor site tends to be A/G (91% in human and 92% in mouse) and the preceding
base to a
.B AG
acceptor tends to be C/T [yes with
.BR --splice ].
This trend is evolutionarily conservative, all the way to S. cerevisiae
(PMID:18688272). Specifying this option generally leads to higher junction
accuracy by several percents, so it is applied by default with
.BR --splice .
However, the SIRV control does not honor this trend
(only ~60%). This option reduces accuracy. If you are benchmarking minimap2
on SIRV data, please add
.B --splice-flank=no
to the command line.
.SS Input/output options
.TP 10
.B -a
Generate CIGAR and output alignments in the SAM format. Minimap2 outputs in PAF
by default.
.TP
.B -Q
Ignore base quality in the input file.
.TP
.B -L
Write CIGAR with >65535 operators at the CG tag. Older tools are unable to
convert alignments with >65535 CIGAR ops to BAM. This option makes minimap2 SAM
compatible with older tools. Newer tools recognizes this tag and reconstruct
the real CIGAR in memory.
.TP
.BI -R \ STR
SAM read group line in a format like
.B @RG\\\\tID:foo\\\\tSM:bar
[].
.TP
.B -c
Generate CIGAR. In PAF, the CIGAR is written to the `cg' custom tag.
.TP
.BI --cs[= STR ]
Output the
.B cs
tag.
.I STR
can be either
.I short
or
.IR long .
If no
.I STR
is given,
.I short
is assumed. [none]
.TP
.B -Y
In SAM output, use soft clipping for supplementary alignments.
.TP
.BI --seed \ INT
Integer seed for randomizing equally best hits. Minimap2 hashes
.I INT
and read name when choosing between equally best hits. [11]
.TP
.BI -t \ INT
Number of threads [3]. Minimap2 uses at most three threads when indexing target
sequences, and uses up to
.IR INT +1
threads when mapping (the extra thread is for I/O, which is frequently idle and
takes little CPU time).
.TP
.B -2
Use two I/O threads during mapping. By default, minimap2 uses one I/O thread.
When I/O is slow (e.g. piping to gzip, or reading from a slow pipe), the I/O
thread may become the bottleneck. Apply this option to use one thread for input
and another thread for output, at the cost of increased peak RAM.
.TP
.BI -K \ NUM
Number of bases loaded into memory to process in a mini-batch [500M].
Similar to option
.BR -I ,
K/M/G/k/m/g suffix is accepted. A large
.I NUM
helps load balancing in the multi-threading mode, at the cost of increased
memory.
.TP
.BR --secondary [= yes | no ]
Whether to output secondary alignments [yes]
.TP
.B --version
Print version number to stdout
.SS Preset options
.TP 10
.BI -x \ STR
Preset []. This option applies multiple options at the same time. It should be
applied before other options because options applied later will overwrite the
values set by
.BR -x .
Available
.I STR
are:
.RS
.TP 8
.B map-pb
PacBio/Oxford Nanopore read to reference mapping
.RB ( -Hk19 )
.TP
.B map-ont
Slightly more sensitive for Oxford Nanopore to reference mapping
.RB ( -k15 ).
For PacBio reads, HPC minimizers consistently leads to faster performance and
more sensitive results in comparison to normal minimizers. For Oxford Nanopore
data, normal minimizers are better, though not much. The effectiveness of HPC
is determined by the sequencing error mode.
.TP
.B asm5
Long assembly to reference mapping
.RB ( -k19
.B -w19 -A1 -B19 -O39,81 -E3,1 -s200
.BR -z200 ).
Typically, the alignment will not extend to regions with 5% or higher sequence
divergence. Only use this preset if the average divergence is far below 5%.
.TP
.B asm10
Long assembly to reference mapping
.RB ( -k19
.B -w19 -A1 -B9 -O16,41 -E2,1 -s200
.BR -z200 ).
Up to 10% sequence divergence.
.TP
.B ava-pb
PacBio all-vs-all overlap mapping
.RB ( -Hk19
.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
.BR 25 ).
.TP
.B ava-ont
Oxford Nanopore all-vs-all overlap mapping
.RB ( -k15
.B -w5 -Xp0 -m100 -g10000 --max-chain-skip
.BR 25 ).
Similarly, the major difference from
.B ava-pb
is that this preset is not using HPC minimizers.
.TP
.B splice
Long-read spliced alignment
.RB ( -k15
.B -w5 --splice -g2000 -G200k -A1 -B2 -O2,32 -E1,0 -C9 -z200 -ub
.BR --splice-flank=yes ).
In the splice mode, 1) long deletions are taken as introns and represented as
the
.RB ` N '
CIGAR operator; 2) long insertions are disabled; 3) deletion and insertion gap
costs are different during chaining; 4) the computation of the
.RB ` ms '
tag ignores introns to demote hits to pseudogenes.
.TP
.B sr
Short single-end reads without splicing
.RB ( -k21
.B -w11 --sr --frag -A2 -B8 -O12,32 -E2,1 -r50 -p.5 -N20 -f1000,5000 -n2 -m20
.B -s40 -g200 -2K50m
.BR --secondary=no ).
.RE
.SS Miscellaneous options
.TP 10
.B --no-kalloc
Use the libc default allocator instead of the kalloc thread-local allocator.
This debugging option is mostly used with Valgrind to detect invalid memory
accesses. Minimap2 runs slower with this option, especially in the
multi-threading mode.
.TP
.B --print-qname
Print query names to stderr, mostly to see which query is crashing minimap2.
.TP
.B --print-seeds
Print seed positions to stderr, for debugging only.
.SH OUTPUT FORMAT
.PP
Minimap2 outputs mapping positions in the Pairwise mApping Format (PAF) by
default. PAF is a TAB-delimited text format with each line consisting of at
least 12 fields as are described in the following table:
.TS
center box;
cb | cb | cb
r | c | l .
Col	Type	Description
_
1	string	Query sequence name
2	int	Query sequence length
3	int	Query start coordinate (0-based)
4	int	Query end coordinate (0-based)
5	char	`+' if query/target on the same strand; `-' if opposite
6	string	Target sequence name
7	int	Target sequence length
8	int	Target start coordinate on the original strand
9	int	Target end coordinate on the original strand
10	int	Number of matching bases in the mapping
11	int	Number bases, including gaps, in the mapping
12	int	Mapping quality (0-255 with 255 for missing)
.TE

.PP
When alignment is available, column 11 gives the total number of sequence
matches, mismatches and gaps in the alignment; column 10 divided by column 11
gives the BLAST-like alignment identity. When alignment is unavailable,
these two columns are approximate. PAF may optionally have additional fields in
the SAM-like typed key-value format. Minimap2 may output the following tags:
.TS
center box;
cb | cb | cb
r | c | l .
Tag	Type	Description
_
tp	A	Type of aln: P/primary, S/secondary and I/inversion
cm	i	Number of minimizers on the chain
s1	i	Chaining score
s2	i	Chaining score of the best secondary chain
NM	i	Total number of mismatches and gaps in the alignment
AS	i	DP alignment score
ms	i	DP score of the max scoring segment in the alignment
nn	i	Number of ambiguous bases in the alignment
ts	A	Transcript strand (splice mode only)
cg	Z	CIGAR string (only in PAF)
cs	Z	Difference string
.TE

.PP
The
.B cs
tag encodes difference sequences in the short form or the entire query
.I AND
reference sequences in the long form. It consists of a series of operations:
.TS
center box;
cb | cb |cb
r | l | l .
Op	Regex	Description
_
 =	[ACGTN]+	Identical sequence (long form)
 :	[0-9]+	Identical sequence length
 *	[acgtn][acgtn]	Substitution: ref to query
 +	[acgtn]+	Insertion to the reference
 -	[acgtn]+	Deletion from the reference
 ~	[acgtn]{2}[0-9]+[acgtn]{2}	Intron length and splice signal
.TE

.SH LIMITATIONS
.TP 2
*
Minimap2 may produce suboptimal alignments through long low-complexity regions
where seed positions may be suboptimal. This should not be a big concern
because even the optimal alignment may be wrong in such regions.
.TP
*
Minimap2 requires SSE2 instructions to compile. It is possible to add
non-SSE2 support, but it would make minimap2 slower by several times.
.SH SEE ALSO
.PP
miniasm(1), minimap(1), bwa(1).
